Complex population structure revealed using genomic data from Tamanend’s bottlenose dolphins (Tursiops erebennus)

Abstract In the waters of North Carolina, on the United States east coast, Tamanend’s bottlenose dolphin ( Tursiops erebennus ) is managed as four stocks, differentiated largely based on photo-identification and satellite telemetry data. Two of the stocks reside primarily within estuarine habitats throughout the year, and two others inhabit coastal waters and make broad scale, migratory movements. The spatio-temporal overlap of these stocks in North Carolina varies seasonally, creating a complicated scenario in which stock boundaries are difficult to identify, and the demographic independence among groups is not well understood. Furthermore, incidental mortality and serious injury of dolphins occurs in several North Carolina fisheries, but the spatio-temporal overlap of the four stocks makes it difficult to assign mortalities and characterize their impact on each stock. To investigate population structure in this complex environment, we obtained biopsy samples from Tamanend’s bottlenose dolphins, and utilized next-generation molecular sequencing to produce a data set of over 6,000 single nucleotide polymorphism markers. Cluster and migration analyses supported the presence of four demographically independent populations. However, the distributions of these populations do not align well with the currently delineated stocks. Instead, our analyses support the existence of three populations in estuarine waters of North Carolina and one inhabiting coastal waters. An improved understanding of the underlying population structure of Tamanend’s bottlenose dolphins in these waters will provide a better characterization of stock distribution and support more accurate assignment of mortality, which is necessary for successful conservation and management of this species.